198c9b8daecc44fbda6a6494c566c723920f030a
lrnassar
  Wed Mar 11 18:25:21 2026 -0700
Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.

diff --git src/hg/hgLiftOver/hgLiftOver.c src/hg/hgLiftOver/hgLiftOver.c
index 2285bd80515..185a4765863 100644
--- src/hg/hgLiftOver/hgLiftOver.c
+++ src/hg/hgLiftOver/hgLiftOver.c
@@ -169,56 +169,56 @@
 
 cgiSimpleTableRowStart();
 cgiTableField("Allow multiple output regions:");
 cgiSimpleTableFieldStart();
 cgiMakeCheckBox(HGLFT_MULTIPLE,multiple);
 puts(" ");
 printInfoIcon("By default, input regions that map to multiple regions will not be lifted at all. When this option is checked, all targets are output.");
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("  Minimum hit size in query:");
 cgiSimpleTableFieldStart();
 cgiMakeIntVar(HGLFT_MINSIZEQ,(keepSettings) ? minSizeQ : chain->minSizeQ,4);
 puts(" ");
-printInfoIcon("In multiple output mode, repeated regions within longer input regions can lead to artifacts. The 'hit size' filter allows to keep only targets with a certain length.");
+printInfoIcon("In multiple output mode, repeated regions within longer input regions can lead to artifacts. The 'hit size' filter allows you to keep only targets with a certain length.");
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("  Minimum chain size in target:");
 cgiSimpleTableFieldStart();
 cgiMakeIntVar(HGLFT_MINCHAINT,(keepSettings) ? minChainT : chain->minChainT,4);
 puts(" ");
 printInfoIcon("In multiple output mode, keeps only targets lifted through alignments of a certain length. At higher phylogenetic distances (e.g. human/mouse), the filters can be useful to keep all copies of the input regions but remove dozens of new small targets introduced by a repeat/transposon within a longer input region.");
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("<B>Regions with an exon-intron structure (usually transcripts, BED 12)</B>");
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("Minimum ratio of alignment blocks or exons that must map:");
 cgiSimpleTableFieldStart();
 cgiMakeDoubleVar(HGLFT_MINBLOCKS,(keepSettings) ? minBlocks : chain->minBlocks,6);
 puts("&nbsp;");
-printInfoIcon("The minimum ratio of the number of exons (not their bases) covered by the alignment. Transcripts lower than this will not be output at all. If an exon (range thickStart-thickEnd) is not alignable at all, it will be skipped or, if the option below is checked, lifted it to the closest alignable base.");
+printInfoIcon("The minimum ratio of the number of exons (not their bases) covered by the alignment. Transcripts lower than this will not be output at all. If an exon (range thickStart-thickEnd) is not alignable at all, it will be skipped or, if the option below is checked, lifted to the closest alignable base.");
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableField("If exon is not mapped, use the closest mapped base:");
 cgiSimpleTableFieldStart();
 cgiMakeCheckBox(HGLFT_FUDGETHICK,(keepSettings) ? fudgeThick : (chain->fudgeThick[0]=='Y'));
 puts("&nbsp;");
 printInfoIcon("If checked, exons that are not covered by an alignment will be lifted to the closest alignable base.");
 cgiTableFieldEnd();
 cgiTableRowEnd();
 
 cgiSimpleTableRowStart();
 cgiTableRowEnd();